JAL-2018 export graduated feature colours correctly

[jalview.git] / src / jalview / gui / FeatureSettings.java

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6ca0769..f250583 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -28,7 +28,9 @@ import jalview.gui.Help.HelpId;
 import jalview.io.JalviewFileChooser;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
+import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.util.QuickSort;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
@@ -58,6 +60,7 @@ import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
 
@@ -169,7 +172,7 @@ public class FeatureSettings extends JPanel implements
       public void mousePressed(MouseEvent evt)
       {
         selectedRow = table.rowAtPoint(evt.getPoint());
-        if (SwingUtilities.isRightMouseButton(evt))
+        if (evt.isPopupTrigger())
         {
           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
@@ -277,7 +280,8 @@ public class FeatureSettings extends JPanel implements
   }
 
   protected void popupSort(final int selectedRow, final String type,
-          final Object typeCol, final Hashtable minmax, int x, int y)
+          final Object typeCol, final Map<String, float[][]> minmax, int x,
+          int y)
   {
     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
             "label.settings_for_param", new String[] { type }));
@@ -312,7 +316,7 @@ public class FeatureSettings extends JPanel implements
     men.add(dens);
     if (minmax != null)
     {
-      final Object typeMinMax = minmax.get(type);
+      final float[][] typeMinMax = minmax.get(type);
       /*
        * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
        * this is broken at the moment and isn't that useful anyway!
@@ -327,7 +331,7 @@ public class FeatureSettings extends JPanel implements
        * 
        * men.add(chb);
        */
-      if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+      if (typeMinMax != null && typeMinMax[0] != null)
       {
         // if (table.getValueAt(row, column));
         // graduated colourschemes for those where minmax exists for the
@@ -392,7 +396,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_containing"));
     selCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -404,7 +407,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_not_containing"));
     clearCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -412,8 +414,30 @@ public class FeatureSettings extends JPanel implements
                 false, type);
       }
     });
+    JMenuItem hideCols = new JMenuItem(
+            MessageManager.getString("label.hide_columns_containing"));
+    hideCols.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.hideFeatureColumns(type, true);
+      }
+    });
+    JMenuItem hideOtherCols = new JMenuItem(
+            MessageManager.getString("label.hide_columns_not_containing"));
+    hideOtherCols.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.hideFeatureColumns(type, false);
+      }
+    });
     men.add(selCols);
     men.add(clearCols);
+    men.add(hideCols);
+    men.add(hideOtherCols);
     men.show(table, x, y);
   }
 
@@ -808,7 +832,7 @@ public class FeatureSettings extends JPanel implements
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            Cache.getProperty("LAST_DIRECTORY"),
             new String[] { "fc" },
             new String[] { "Sequence Feature Colours" },
             "Sequence Feature Colours");
@@ -829,34 +853,35 @@ public class FeatureSettings extends JPanel implements
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(choice), "UTF-8"));
 
-        Set fr_colours = fr.getAllFeatureColours();
-        Iterator e = fr_colours.iterator();
+        Set<String> fr_colours = fr.getAllFeatureColours();
+        Iterator<String> e = fr_colours.iterator();
         float[] sortOrder = new float[fr_colours.size()];
         String[] sortTypes = new String[fr_colours.size()];
         int i = 0;
         while (e.hasNext())
         {
-          sortTypes[i] = e.next().toString();
+          sortTypes[i] = e.next();
           sortOrder[i] = fr.getOrder(sortTypes[i]);
           i++;
         }
-        jalview.util.QuickSort.sort(sortOrder, sortTypes);
+        QuickSort.sort(sortOrder, sortTypes);
         sortOrder = null;
         Object fcol;
         GraduatedColor gcol;
-        for (i = 0; i < sortTypes.length; i++)
+        for (String featureType : sortTypes)
         {
           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
-          col.setName(sortTypes[i]);
-          col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
-                  .getName())));
-          fcol = fr.getFeatureStyle(sortTypes[i]);
+          col.setName(featureType);
+          fcol = fr.getFeatureStyle(featureType);
+          Color colour = fcol instanceof Color ? (Color) fcol
+                  : ((GraduatedColor) fcol).getMaxColor();
+          col.setRGB(Format.getHexString(colour));
           if (fcol instanceof GraduatedColor)
           {
             gcol = (GraduatedColor) fcol;
             col.setMin(gcol.getMin());
             col.setMax(gcol.getMax());
-            col.setMinRGB(jalview.util.Format.getHexString(gcol
+            col.setMinRGB(Format.getHexString(gcol
                     .getMinColor()));
             col.setAutoScale(gcol.isAutoScale());
             col.setThreshold(gcol.getThresh());